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root/OpenMD/branches/development/src/io/RestReader.cpp

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trunk/src/io/RestReader.cpp (file contents), Revision 990 by chrisfen, Mon Jun 19 01:36:06 2006 UTC vs.
branches/development/src/io/RestReader.cpp (file contents), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

#	Line 1 | Line 1
1	<	/*
2	<	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3	<	*
1	>	/*
2	>	* Copyright (c) 2009 The University of Notre Dame. All Rights Reserved.
3	>	*
4		* The University of Notre Dame grants you ("Licensee") a
5		* non-exclusive, royalty free, license to use, modify and
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	<	*/
31	>	*
32	>	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	>	* research, please cite the appropriate papers when you publish your
34	>	* work.  Good starting points are:
35	>	*
36	>	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	>	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	>	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	>	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	>	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	>	*/
42
43	<	#define _LARGEFILE_SOURCE64
44	<	#define _FILE_OFFSET_BITS 64
45	<
46	<	#include <sys/types.h>
47	<	#include <sys/stat.h>
48	<
49	<	#include <iostream>
50	<	#include <math.h>
51	<
52	<	#include <stdio.h>
53	<	#include <stdlib.h>
54	<	#include <string.h>
55	<
56	<	#include "primitives/Molecule.hpp"
57	<	#include "utils/MemoryUtils.hpp"
43	>
44	>	#include <sys/types.h>
45	>	#include <sys/stat.h>
46	>
47	>	#include <math.h>
48	>	#include <string>
49	>	#include <sstream>
50	>	#include <iostream>
51	>	#include <stdio.h>
52	>	#include <stdlib.h>
53	>	#include <string.h>
54	>
55	>	#include "io/RestReader.hpp"
56	>	#include "primitives/Molecule.hpp"
57	>	#include "utils/simError.h"
58	>	#include "utils/MemoryUtils.hpp"
59		#include "utils/StringTokenizer.hpp"
60	<	#include "io/RestReader.hpp"
61	<	#include "utils/simError.h"
60	>	#include "restraints/ObjectRestraint.hpp"
61	>	#include "restraints/MolecularRestraint.hpp"
62	>
63	>	#ifdef IS_MPI
64	>
65	>	#include <mpi.h>
66	>	#endif
67
68	<	#ifdef IS_MPI
62	<	#include <mpi.h>
63	<	#define TAKE_THIS_TAG_CHAR 0
64	<	#define TAKE_THIS_TAG_INT 1
65	<	#define TAKE_THIS_TAG_DOUBLE 2
66	<	#endif // is_mpi
68	>	namespace OpenMD {
69
70	<	namespace oopse {
71	<
72	<	RestReader::RestReader( SimInfo* info ) : info_(info){
70	>	void RestReader::scanFile(){
71	>	int lineNo = 0;
72	>	std::streampos prevPos;
73	>	std::streampos  currPos;
74
75	<	idealName = "idealCrystal.in";
75	>	#ifdef IS_MPI
76
77	<	isScanned = false;
78	<
79	<	#ifdef IS_MPI
80	<	if (worldRank == 0) {
81	<	#endif
77	>	if (worldRank == 0) {
78	>	#endif // is_mpi
79	>
80	>	inFile_->clear();
81	>	currPos = inFile_->tellg();
82	>	prevPos = currPos;
83
84	<	inIdealFile = fopen(idealName, "r");
85	<	if(inIdealFile == NULL){
86	<	sprintf(painCave.errMsg,
87	<	"RestReader: Cannot open file: %s\n", idealName);
88	<	painCave.isFatal = 1;
89	<	simError();
84	>	bool foundOpenSnapshotTag = false;
85	>
86	>	while(!foundOpenSnapshotTag && inFile_->getline(buffer, bufferSize)) {
87	>	++lineNo;
88	>
89	>	std::string line = buffer;
90	>	currPos = inFile_->tellg();
91	>	if (line.find("<Snapshot>")!= std::string::npos) {
92	>	foundOpenSnapshotTag = true;
93	>	framePos_ = prevPos;
94	>	}
95	>	prevPos = currPos;
96		}
97
98	<	inIdealFileName = idealName;
89	<	#ifdef IS_MPI
98	>	#ifdef IS_MPI
99		}
100	<	strcpy( checkPointMsg,
101	<	"File \"idealCrystal.in\" opened successfully for reading." );
102	<	MPIcheckPoint();
94	<	#endif
100	>	MPI_Bcast(&framePos_, 1, MPI_INT, 0, MPI_COMM_WORLD);
101	>	#endif // is_mpi
102	>	}
103
104	<	return;
105	<	}
106	<
107	<	RestReader :: ~RestReader( ){
108	<	#ifdef IS_MPI
109	<	if (worldRank == 0) {
110	<	#endif
111	<	int error;
112	<	error = fclose( inIdealFile );
104	>
105	>	void RestReader::readSet(){
106	>	std::string line;
107	>
108	>	#ifndef IS_MPI
109	>
110	>	inFile_->clear();
111	>	inFile_->seekg(framePos_);
112	>
113	>	std::istream& inputStream = *inFile_;
114	>	#else
115	>
116	>	int masterNode = 0;
117	>	std::stringstream sstream;
118	>	if (worldRank == masterNode) {
119	>	std::string sendBuffer;
120
121	<	if( error ){
122	<	sprintf( painCave.errMsg,
123	<	"Error closing %s\n", inIdealFileName.c_str());
124	<	simError();
121	>	inFile_->clear();
122	>	inFile_->seekg(framePos_);
123	>
124	>	while (inFile_->getline(buffer, bufferSize)) {
125	>
126	>	line = buffer;
127	>	sendBuffer += line;
128	>	sendBuffer += '\n';
129	>	if (line.find("</Snapshot>") != std::string::npos) {
130	>	break;
131	>	}
132		}
133
134	<	MemoryUtils::deletePointers(framePos);
134	>	int sendBufferSize = sendBuffer.size();
135	>	MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
136	>	MPI_Bcast((void *)sendBuffer.c_str(), sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
137
138	<	#ifdef IS_MPI
139	<	}
140	<	strcpy( checkPointMsg, "Restraint file closed successfully." );
141	<	MPIcheckPoint();
138	>	sstream.str(sendBuffer);
139	>	} else {
140	>	int sendBufferSize;
141	>	MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
142	>	char * recvBuffer = new char[sendBufferSize+1];
143	>	assert(recvBuffer);
144	>	recvBuffer[sendBufferSize] = '\0';
145	>	MPI_Bcast(recvBuffer, sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
146	>	sstream.str(recvBuffer);
147	>	delete [] recvBuffer;
148	>	}
149	>
150	>	std::istream& inputStream = sstream;
151		#endif
152
153	<	return;
121	<	}
122	<
123	<
124	<	void RestReader :: readIdealCrystal(){
125	<
126	<	int i;
127	<	unsigned int j;
153	>	inputStream.getline(buffer, bufferSize);
154
155	<	#ifdef IS_MPI
156	<	int done, which_node, which_atom; // loop counter
157	<	#endif //is_mpi
155	>	line = buffer;
156	>	if (line.find("<Snapshot>") == std::string::npos) {
157	>	sprintf(painCave.errMsg,
158	>	"RestReader Error: can not find <Snapshot>\n");
159	>	painCave.isFatal = 1;
160	>	simError();
161	>	}
162
163	<	const int BUFFERSIZE = 2000; // size of the read buffer
164	<	int nTotObjs; // the number of atoms
135	<	char read_buffer[BUFFERSIZE]; //the line buffer for reading
163	>	//read frameData
164	>	readFrameProperties(inputStream);
165
166	<	char *eof_test; // ptr to see when we reach the end of the file
167	<	char *parseErr;
166	>	//read StuntDoubles
167	>	readStuntDoubles(inputStream);
168
169	<	std::vector<StuntDouble*> integrableObjects;
169	>	inputStream.getline(buffer, bufferSize);
170	>	line = buffer;
171	>	if (line.find("</Snapshot>") == std::string::npos) {
172	>	sprintf(painCave.errMsg,
173	>	"RestReader Error: can not find </Snapshot>\n");
174	>	painCave.isFatal = 1;
175	>	simError();
176	>	}
177	>	}
178
179	+	void RestReader::readReferenceStructure() {
180	+
181	+	// We need temporary storage to keep track of all StuntDouble positions
182	+	// in case some of the restraints are molecular (i.e. if they use
183	+	// multiple SD positions to determine restrained orientations or positions:
184	+
185	+	all_pos_.clear();
186	+	all_pos_.resize(info_->getNGlobalIntegrableObjects()) ;
187	+
188	+	// Restraint files are just standard dump files, but with the reference
189	+	// structure stored in the first frame (frame 0).
190	+	// RestReader overloads readSet and explicitly handles all of the
191	+	// ObjectRestraints in that method:
192	+
193	+	scanFile();
194	+
195	+	readSet();
196	+
197	+
198	+	// all ObjectRestraints have been handled, now we have to worry about
199	+	// molecular restraints:
200	+
201	+	SimInfo::MoleculeIterator i;
202	+	Molecule::IntegrableObjectIterator j;
203		Molecule* mol;
204	<	StuntDouble* integrableObject;
144	<	SimInfo::MoleculeIterator mi;
145	<	Molecule::IntegrableObjectIterator ii;
204	>	StuntDouble* sd;
205
206	<	#ifndef IS_MPI
206	>	// no need to worry about parallel molecules, as molecules are not
207	>	// split across processor boundaries.  Just loop over all molecules
208	>	// we know about:
209
210	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inIdealFile);
211	<	if( eof_test == NULL ){
151	<	sprintf( painCave.errMsg,
152	<	"RestraintReader error: error reading 1st line of \"%s\"\n",
153	<	inIdealFileName.c_str() );
154	<	painCave.isFatal = 1;
155	<	simError();
156	<	}
157	<
158	<	nTotObjs = atoi( read_buffer );
159	<
160	<	if( nTotObjs != info_->getNGlobalIntegrableObjects() ){
161	<	sprintf( painCave.errMsg,
162	<	"RestraintReader error. %s nIntegrable, %d, "
163	<	"does not match the meta-data file's nIntegrable, %d.\n",
164	<	inIdealFileName.c_str(), nTotObjs,
165	<	info_->getNGlobalIntegrableObjects());
166	<	painCave.isFatal = 1;
167	<	simError();
168	<	}
169	<
170	<	// skip over the comment line
171	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inIdealFile);
172	<	if(eof_test == NULL){
173	<	sprintf( painCave.errMsg,
174	<	"error in reading commment in %s\n", inIdealFileName.c_str());
175	<	painCave.isFatal = 1;
176	<	simError();
177	<	}
178	<
179	<	// parse the ideal crystal lines
180	<	/*
181	<	* Note: we assume that there is a one-to-one correspondence between
182	<	* integrable objects and lines in the idealCrystal.in file.  Thermodynamic
183	<	* integration is only supported for simple rigid bodies.
184	<	*/
185	<	for (mol = info_->beginMolecule(mi); mol != NULL;
186	<	mol = info_->nextMolecule(mi)) {
210	>	for (mol = info_->beginMolecule(i); mol != NULL;
211	>	mol = info_->nextMolecule(i)) {
212
213	<	for (integrableObject = mol->beginIntegrableObject(ii);
214	<	integrableObject != NULL;
215	<	integrableObject = mol->nextIntegrableObject(ii)) {
213	>	// is this molecule restrained?
214	>	GenericData* data = mol->getPropertyByName("Restraint");
215	>
216	>	if (data != NULL) {
217
218	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inIdealFile);
193	<	if(eof_test == NULL){
194	<	sprintf(painCave.errMsg,
195	<	"RestReader Error: error in reading file %s\n"
196	<	"natoms  = %d; index = %d\n"
197	<	"error reading the line from the file.\n",
198	<	inIdealFileName.c_str(), nTotObjs,
199	<	integrableObject->getGlobalIndex() );
200	<	painCave.isFatal = 1;
201	<	simError();
202	<	}
218	>	// make sure we can reinterpret the generic data as restraint data:
219
220	<	parseErr = parseIdealLine( read_buffer, integrableObject);
205	<	if( parseErr != NULL ){
206	<	strcpy( painCave.errMsg, parseErr );
207	<	painCave.isFatal = 1;
208	<	simError();
209	<	}
210	<	}
211	<	}
212	<
213	<	// MPI Section of code..........
214	<	#else //IS_MPI
215	<
216	<	// first thing first, suspend fatalities.
217	<	painCave.isEventLoop = 1;
218	<
219	<	int masterNode = 0;
220	<	int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
221	<
222	<	MPI_Status istatus;
223	<	int nCurObj;
224	<	int nitems;
225	<	int haveError;
226	<
227	<	nTotObjs = info_->getNGlobalIntegrableObjects();
228	<	haveError = 0;
229	<
230	<	if (worldRank == masterNode) {
231	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inIdealFile);
232	<	if( eof_test == NULL ){
233	<	sprintf( painCave.errMsg,
234	<	"Error reading 1st line of %s \n ",inIdealFileName.c_str());
235	<	painCave.isFatal = 1;
236	<	simError();
237	<	}
238	<
239	<	nitems = atoi( read_buffer );
240	<
241	<	// Check to see that the number of integrable objects in the
242	<	// intial configuration file is the same as derived from the
243	<	// meta-data file.
244	<	if( nTotObjs != nitems){
245	<	sprintf( painCave.errMsg,
246	<	"RestraintReader Error. %s nIntegrable, %d, "
247	<	"does not match the meta-data file's nIntegrable, %d.\n",
248	<	inIdealFileName.c_str(), nTotObjs,
249	<	info_->getNGlobalIntegrableObjects());
250	<	painCave.isFatal = 1;
251	<	simError();
252	<	}
253	<
254	<	// skip over the comment line
255	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inIdealFile);
256	<	if(eof_test == NULL){
257	<	sprintf( painCave.errMsg,
258	<	"error in reading commment in %s\n", inIdealFileName.c_str());
259	<	painCave.isFatal = 1;
260	<	simError();
261	<	}
262	<
263	<	MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, masterNode, MPI_COMM_WORLD);
264	<
265	<	for (i=0 ; i < info_->getNGlobalMolecules(); i++) {
266	<	int which_node = info_->getMolToProc(i);
220	>	RestraintData* restData= dynamic_cast<RestraintData*>(data);
221
222	<	if(which_node == masterNode){
269	<	//molecules belong to master node
222	>	if (restData != NULL) {
223
224	<	mol = info_->getMoleculeByGlobalIndex(i);
224	>	// make sure we can reinterpet the restraint data as a
225	>	// pointer to a MolecularRestraint:
226
227	<	if(mol == NULL) {
274	<	sprintf(painCave.errMsg,
275	<	"RestReader Error: Molecule not found on node %d!\n",
276	<	worldRank);
277	<	painCave.isFatal = 1;
278	<	simError();
279	<	}
227	>	MolecularRestraint* mRest = dynamic_cast<MolecularRestraint*>(restData->getData());
228
229	<	for (integrableObject = mol->beginIntegrableObject(ii);
282	<	integrableObject != NULL;
283	<	integrableObject = mol->nextIntegrableObject(ii)){
229	>	if (mRest != NULL) {
230
231	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inIdealFile);
231	>	// now we need to pack the stunt doubles for the reference
232	>	// structure:
233
234	<	if(eof_test == NULL){
235	<	sprintf(painCave.errMsg,
236	<	"RestReader Error: error in reading file %s\n"
237	<	"natoms  = %d; index = %d\n"
291	<	"error reading the line from the file.\n",
292	<	inIdealFileName.c_str(), nTotObjs, i );
293	<	painCave.isFatal = 1;
294	<	simError();
295	<	}
296	<
297	<	parseIdealLine(read_buffer, integrableObject);
298	<
299	<	}
300	<
301	<	} else {
302	<	//molecule belongs to slave nodes
303	<
304	<	MPI_Recv(&nCurObj, 1, MPI_INT, which_node,
305	<	TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
306	<
307	<	for(j = 0; j < nCurObj; j++){
234	>	std::vector<Vector3d> ref;
235	>	int count = 0;
236	>	RealType mass, mTot;
237	>	Vector3d COM(0.0);
238
239	<	eof_test = fgets(read_buffer, sizeof(read_buffer), inIdealFile);
310	<	if(eof_test == NULL){
311	<	sprintf(painCave.errMsg,
312	<	"RestReader Error: error in reading file %s\n"
313	<	"natoms  = %d; index = %d\n"
314	<	"error reading the line from the file.\n",
315	<	inIdealFileName.c_str(), nTotObjs, i );
316	<	painCave.isFatal = 1;
317	<	simError();
318	<	}
239	>	mTot = 0.0;
240
241	<	MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node,
242	<	TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
241	>	// loop over the stunt doubles in this molecule in the order we
242	>	// will be looping them in the restraint code:
243	>
244	>	for (sd = mol->beginIntegrableObject(j); sd != NULL;
245	>	sd = mol->nextIntegrableObject(j)) {
246	>
247	>	// push back the reference positions of the stunt
248	>	// doubles from the *globally* sorted array of
249	>	// positions:
250	>
251	>	ref.push_back( all_pos_[sd->getGlobalIntegrableObjectIndex()] );
252	>	mass = sd->getMass();
253	>	COM = COM + mass * ref[count];
254	>	mTot = mTot + mass;
255	>	count = count + 1;
256	>	}
257	>	COM /= mTot;
258	>	mRest->setReferenceStructure(ref, COM);
259		}
260		}
261		}
262	<	} else {
263	<	//actions taken at slave nodes
327	<	MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, masterNode, MPI_COMM_WORLD);
262	>	}
263	>	}
264
265	<	for (i=0 ; i < info_->getNGlobalMolecules(); i++) {
266	<	int which_node = info_->getMolToProc(i);
265	>
266	>
267	>	void RestReader::parseDumpLine(const std::string& line) {
268
269	<	if(which_node == worldRank){
270	<	//molecule with global index i belongs to this processor
269	>	StringTokenizer tokenizer(line);
270	>	int nTokens;
271	>
272	>	nTokens = tokenizer.countTokens();
273	>
274	>	if (nTokens < 2) {
275	>	sprintf(painCave.errMsg,
276	>	"RestReader Error: Not enough Tokens.\n%s\n", line.c_str());
277	>	painCave.isFatal = 1;
278	>	simError();
279	>	}
280	>
281	>	int index = tokenizer.nextTokenAsInt();
282	>
283	>	StuntDouble* integrableObject = info_->getIOIndexToIntegrableObject(index);
284	>
285	>	if (integrableObject == NULL) {
286	>	return;
287	>	}
288	>
289	>	std::string type = tokenizer.nextToken();
290	>	int size = type.size();
291	>
292	>	Vector3d pos;
293	>	Quat4d q;
294	>
295	>	for(int i = 0; i < size; ++i) {
296	>	switch(type[i]) {
297	>
298	>	case 'p': {
299	>	pos[0] = tokenizer.nextTokenAsDouble();
300	>	pos[1] = tokenizer.nextTokenAsDouble();
301	>	pos[2] = tokenizer.nextTokenAsDouble();
302	>	break;
303	>	}
304	>	case 'v' : {
305	>	Vector3d vel;
306	>	vel[0] = tokenizer.nextTokenAsDouble();
307	>	vel[1] = tokenizer.nextTokenAsDouble();
308	>	vel[2] = tokenizer.nextTokenAsDouble();
309	>	break;
310	>	}
311	>
312	>	case 'q' : {
313	>	if (integrableObject->isDirectional()) {
314
315	<	mol = info_->getMoleculeByGlobalIndex(i);
315	>	q[0] = tokenizer.nextTokenAsDouble();
316	>	q[1] = tokenizer.nextTokenAsDouble();
317	>	q[2] = tokenizer.nextTokenAsDouble();
318	>	q[3] = tokenizer.nextTokenAsDouble();
319
320	<	if(mol == NULL) {
321	<	sprintf(painCave.errMsg,
339	<	"RestReader Error: molecule not found on node %d\n",
340	<	worldRank);
341	<	painCave.isFatal = 1;
342	<	simError();
343	<	}
344	<
345	<	nCurObj = mol->getNIntegrableObjects();
346	<
347	<	MPI_Send(&nCurObj, 1, MPI_INT, masterNode,
348	<	TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
349	<
350	<	for (integrableObject = mol->beginIntegrableObject(ii);
351	<	integrableObject != NULL;
352	<	integrableObject = mol->nextIntegrableObject(ii)){
320	>	RealType qlen = q.length();
321	>	if (qlen < OpenMD::epsilon) { //check quaternion is not equal to 0
322
323	<	MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, masterNode,
324	<	TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
325	<
326	<	parseErr = parseIdealLine(read_buffer, integrableObject);
327	<
328	<	if( parseErr != NULL ){
329	<	strcpy( painCave.errMsg, parseErr );
330	<	simError();
323	>	sprintf(painCave.errMsg,
324	>	"RestReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2) ~ 0\n");
325	>	painCave.isFatal = 1;
326	>	simError();
327	>	}
328	>
329	>	q.normalize();
330	>	}
331	>	break;
332	>	}
333	>	case 'j' : {
334	>	Vector3d ji;
335	>	if (integrableObject->isDirectional()) {
336	>	ji[0] = tokenizer.nextTokenAsDouble();
337	>	ji[1] = tokenizer.nextTokenAsDouble();
338	>	ji[2] = tokenizer.nextTokenAsDouble();
339	>	}
340	>	break;
341	>	}
342	>	case 'f': {
343	>	Vector3d force;
344	>	force[0] = tokenizer.nextTokenAsDouble();
345	>	force[1] = tokenizer.nextTokenAsDouble();
346	>	force[2] = tokenizer.nextTokenAsDouble();
347	>	break;
348	>	}
349	>	case 't' : {
350	>	Vector3d torque;
351	>	torque[0] = tokenizer.nextTokenAsDouble();
352	>	torque[1] = tokenizer.nextTokenAsDouble();
353	>	torque[2] = tokenizer.nextTokenAsDouble();
354	>	break;
355	>	}
356	>	default: {
357	>	sprintf(painCave.errMsg,
358	>	"RestReader Error: %s is an unrecognized type\n", type.c_str());
359	>	painCave.isFatal = 1;
360	>	simError();
361	>	break;
362	>	}
363	>	}
364	>	// keep the position in case we need it for a molecular restraint:
365	>
366	>	all_pos_[index] = pos;
367	>
368	>	// is this io restrained?
369	>	GenericData* data = integrableObject->getPropertyByName("Restraint");
370	>	ObjectRestraint* oRest;
371	>
372	>	if (data != NULL) {
373	>	// make sure we can reinterpret the generic data as restraint data:
374	>	RestraintData* restData= dynamic_cast<RestraintData*>(data);
375	>	if (restData != NULL) {
376	>	// make sure we can reinterpet the restraint data as a pointer to
377	>	// an ObjectRestraint:
378	>	oRest = dynamic_cast<ObjectRestraint*>(restData->getData());
379	>	if (oRest != NULL) {
380	>	if (integrableObject->isDirectional()) {
381	>	oRest->setReferenceStructure(pos, q.toRotationMatrix3());
382	>	} else {
383	>	oRest->setReferenceStructure(pos);
384		}
385		}
386		}
387		}
388		}
367	–	#endif
389		}
390
391	<	char* RestReader::parseIdealLine(char* readLine, StuntDouble* sd){
391	>	void  RestReader::readStuntDoubles(std::istream& inputStream) {
392
393	<	RealType pos[3];        // position place holders
394	<	RealType q[4];          // the quaternions
374	<	RealType RfromQ[3][3];  // the rotation matrix
375	<	RealType normalize;     // to normalize the reference unit vector
376	<	RealType uX, uY, uZ;    // reference unit vector place holders
377	<	RealType uselessToken;
378	<	StringTokenizer tokenizer(readLine);
379	<	int nTokens;
393	>	inputStream.getline(buffer, bufferSize);
394	>	std::string line(buffer);
395
396	<	nTokens = tokenizer.countTokens();
397	<
398	<	if (nTokens < 14) {
399	<	sprintf(painCave.errMsg,
400	<	"RestReader Error: Not enough Tokens.\n");
386	<	painCave.isFatal = 1;
387	<	simError();
396	>	if (line.find("<StuntDoubles>") == std::string::npos) {
397	>	sprintf(painCave.errMsg,
398	>	"RestReader Error: Missing <StuntDoubles>\n");
399	>	painCave.isFatal = 1;
400	>	simError();
401		}
402
403	<	std::string name = tokenizer.nextToken();
404	<
392	<	if (name != sd->getType()) {
403	>	while(inputStream.getline(buffer, bufferSize)) {
404	>	line = buffer;
405
406	<	sprintf(painCave.errMsg,
407	<	"RestReader Error: Atom type [%s] in %s does not "
408	<	"match Atom Type [%s] in .md file.\n",
409	<	name.c_str(), inIdealFileName.c_str(),
410	<	sd->getType().c_str());
399	<	painCave.isFatal = 1;
400	<	simError();
406	>	if(line.find("</StuntDoubles>") != std::string::npos) {
407	>	break;
408	>	}
409	>
410	>	parseDumpLine(line);
411		}
412
413	<	pos[0] = tokenizer.nextTokenAsDouble();
404	<	pos[1] = tokenizer.nextTokenAsDouble();
405	<	pos[2] = tokenizer.nextTokenAsDouble();
413	>	}
414
415	<	// store the positions in the stuntdouble as generic data doubles
416	<	DoubleGenericData* refPosX = new DoubleGenericData();
417	<	refPosX->setID("refPosX");
418	<	refPosX->setData(pos[0]);
411	<	sd->addProperty(refPosX);
415	>
416	>	void RestReader::readFrameProperties(std::istream& inputStream) {
417	>	inputStream.getline(buffer, bufferSize);
418	>	std::string line(buffer);
419
420	<	DoubleGenericData* refPosY = new DoubleGenericData();
421	<	refPosY->setID("refPosY");
422	<	refPosY->setData(pos[1]);
423	<	sd->addProperty(refPosY);
424	<
425	<	DoubleGenericData* refPosZ = new DoubleGenericData();
419	<	refPosZ->setID("refPosZ");
420	<	refPosZ->setData(pos[2]);
421	<	sd->addProperty(refPosZ);
420	>	if (line.find("<FrameData>") == std::string::npos) {
421	>	sprintf(painCave.errMsg,
422	>	"RestReader Error: Missing <FrameData>\n");
423	>	painCave.isFatal = 1;
424	>	simError();
425	>	}
426
427	<	// we don't need the velocities
428	<	uselessToken = tokenizer.nextTokenAsDouble();
429	<	uselessToken = tokenizer.nextTokenAsDouble();
430	<	uselessToken = tokenizer.nextTokenAsDouble();
431	<
432	<	if (sd->isDirectional()) {
427	>	// restraints don't care about frame data (unless we need to wrap
428	>	// coordinates, but we'll worry about that later), so
429	>	// we'll just scan ahead until the end of the frame data:
430	>
431	>	while(inputStream.getline(buffer, bufferSize)) {
432	>	line = buffer;
433
434	<	q[0] = tokenizer.nextTokenAsDouble();
435	<	q[1] = tokenizer.nextTokenAsDouble();
432	<	q[2] = tokenizer.nextTokenAsDouble();
433	<	q[3] = tokenizer.nextTokenAsDouble();
434	<
435	<	// now build the rotation matrix and find the unit vectors
436	<	RfromQ[0][0] = q[0]*q[0] + q[1]*q[1] - q[2]*q[2] - q[3]*q[3];
437	<	RfromQ[0][1] = 2*(q[1]*q[2] + q[0]*q[3]);
438	<	RfromQ[0][2] = 2*(q[1]*q[3] - q[0]*q[2]);
439	<	RfromQ[1][0] = 2*(q[1]*q[2] - q[0]*q[3]);
440	<	RfromQ[1][1] = q[0]*q[0] - q[1]*q[1] + q[2]*q[2] - q[3]*q[3];
441	<	RfromQ[1][2] = 2*(q[2]*q[3] + q[0]*q[1]);
442	<	RfromQ[2][0] = 2*(q[1]*q[3] + q[0]*q[2]);
443	<	RfromQ[2][1] = 2*(q[2]*q[3] - q[0]*q[1]);
444	<	RfromQ[2][2] = q[0]*q[0] - q[1]*q[1] - q[2]*q[2] + q[3]*q[3];
445	<
446	<	normalize = sqrt(RfromQ[2][0]*RfromQ[2][0] + RfromQ[2][1]*RfromQ[2][1]
447	<	+ RfromQ[2][2]*RfromQ[2][2]);
448	<	uX = RfromQ[2][0]/normalize;
449	<	uY = RfromQ[2][1]/normalize;
450	<	uZ = RfromQ[2][2]/normalize;
451	<
452	<	// store reference unit vectors as generic data in the stuntdouble
453	<	DoubleGenericData* refVectorX = new DoubleGenericData();
454	<	refVectorX->setID("refVectorX");
455	<	refVectorX->setData(uX);
456	<	sd->addProperty(refVectorX);
457	<
458	<	DoubleGenericData* refVectorY = new DoubleGenericData();
459	<	refVectorY->setID("refVectorY");
460	<	refVectorY->setData(uY);
461	<	sd->addProperty(refVectorY);
462	<
463	<	DoubleGenericData* refVectorZ = new DoubleGenericData();
464	<	refVectorZ->setID("refVectorZ");
465	<	refVectorZ->setData(uZ);
466	<	sd->addProperty(refVectorZ);
467	<	}
468	<
469	<	// we don't need the angular velocities, so let's exit the line
470	<	return NULL;
471	<	}
472	<
473	<	void RestReader::readZangle(){
474	<
475	<	int i;
476	<	unsigned int j;
477	<	int isPresent;
478	<
479	<	Molecule* mol;
480	<	StuntDouble* integrableObject;
481	<	SimInfo::MoleculeIterator mi;
482	<	Molecule::IntegrableObjectIterator ii;
483	<
484	<	#ifdef IS_MPI
485	<	int done, which_node, which_atom; // loop counter
486	<	int nProc;
487	<	MPI_Status istatus;
488	<	#endif //is_mpi
489	<
490	<	const int BUFFERSIZE = 2000; // size of the read buffer
491	<	int nTotObjs; // the number of atoms
492	<	char read_buffer[BUFFERSIZE]; //the line buffer for reading
493	<
494	<	char *eof_test; // ptr to see when we reach the end of the file
495	<	char *parseErr;
496	<
497	<	std::vector<StuntDouble*> vecParticles;
498	<	std::vector<RealType> tempZangs;
499	<
500	<	inAngFileName = info_->getRestFileName();
501	<
502	<	inAngFileName += "0";
503	<
504	<	// open the omega value file for reading
505	<	#ifdef IS_MPI
506	<	if (worldRank == 0) {
507	<	#endif
508	<	isPresent = 1;
509	<	inAngFile = fopen(inAngFileName.c_str(), "r");
510	<	if(!inAngFile){
511	<	sprintf(painCave.errMsg,
512	<	"Restraints Warning: %s file is not present\n"
513	<	"\tAll omega values will be initialized to zero. If the\n"
514	<	"\tsimulation is starting from the idealCrystal.in reference\n"
515	<	"\tconfiguration, this is the desired action. If this is not\n"
516	<	"\tthe case, the energy calculations will be incorrect.\n",
517	<	inAngFileName.c_str());
518	<	painCave.severity = OOPSE_WARNING;
519	<	painCave.isFatal = 0;
520	<	simError();
521	<	isPresent = 0;
434	>	if(line.find("</FrameData>") != std::string::npos) {
435	>	break;
436		}
523	–
524	–	#ifdef IS_MPI
525	–	// let the other nodes know the status of the file search
526	–	MPI_Bcast(&isPresent, 1, MPI_INT, 0, MPI_COMM_WORLD);
527	–	#endif // is_mpi
528	–
529	–	if (!isPresent) {
530	–	zeroZangle();
531	–	return;
532	–	}
533	–
534	–	#ifdef IS_MPI
535	–	}
536	–
537	–	// listen to node 0 to see if we should exit this function
538	–	if (worldRank != 0) {
539	–	MPI_Bcast(&isPresent, 1, MPI_INT, 0, MPI_COMM_WORLD);
540	–	if (!isPresent) {
541	–	zeroZangle();
542	–	return;
543	–	}
544	–	}
545	–
546	–	strcpy( checkPointMsg, "zAngle file opened successfully for reading." );
547	–	MPIcheckPoint();
548	–	#endif
549	–
550	–	#ifndef IS_MPI
551	–
552	–	eof_test = fgets(read_buffer, sizeof(read_buffer), inAngFile);
553	–	if( eof_test == NULL ){
554	–	sprintf( painCave.errMsg,
555	–	"RestraintReader error: error reading 1st line of \"%s\"\n",
556	–	inAngFileName.c_str() );
557	–	painCave.isFatal = 1;
558	–	simError();
559	–	}
560	–
561	–	eof_test = fgets(read_buffer, sizeof(read_buffer), inAngFile);
562	–	while ( eof_test != NULL ) {
563	–	// check for and ignore blank lines
564	–	if ( read_buffer != NULL )
565	–	tempZangs.push_back( atof(read_buffer) );
566	–	eof_test = fgets(read_buffer, sizeof(read_buffer), inAngFile);
567	–	}
568	–
569	–	nTotObjs = info_->getNGlobalIntegrableObjects();
570	–
571	–	if( nTotObjs != tempZangs.size() ){
572	–	sprintf( painCave.errMsg,
573	–	"RestraintReader zAngle reading error. %s nIntegrable, %d, "
574	–	"does not match the meta-data file's nIntegrable, %d.\n",
575	–	inAngFileName.c_str(), tempZangs.size(), nTotObjs );
576	–	painCave.isFatal = 1;
577	–	simError();
578	–	}
579	–
580	–	// load the zAngles into the integrable objects
581	–	i = 0;
582	–	for (mol = info_->beginMolecule(mi); mol != NULL;
583	–	mol = info_->nextMolecule(mi)) {
437
585	–	for (integrableObject = mol->beginIntegrableObject(ii);
586	–	integrableObject != NULL;
587	–	integrableObject = mol->nextIntegrableObject(ii)) {
588	–
589	–	integrableObject->setZangle(tempZangs[i]);
590	–	i++;
591	–	}
438		}
439
594	–	// MPI Section of code..........
595	–	#else //IS_MPI
596	–
597	–	// first thing first, suspend fatalities.
598	–	painCave.isEventLoop = 1;
599	–
600	–	int masterNode = 0;
601	–	int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
602	–	int haveError;
603	–	int intObjIndex;
604	–	int intObjIndexTransfer;
605	–
606	–	int nCurObj;
607	–	RealType angleTranfer;
608	–
609	–	nTotObjs = info_->getNGlobalIntegrableObjects();
610	–	haveError = 0;
611	–
612	–	if (worldRank == masterNode) {
613	–
614	–	eof_test = fgets(read_buffer, sizeof(read_buffer), inAngFile);
615	–	if( eof_test == NULL ){
616	–	sprintf( painCave.errMsg,
617	–	"Error reading 1st line of %s \n ",inAngFileName.c_str());
618	–	haveError = 1;
619	–	simError();
620	–	}
621	–
622	–	// let node 0 load the temporary angle vector
623	–	eof_test = fgets(read_buffer, sizeof(read_buffer), inAngFile);
624	–	while ( eof_test != NULL ) {
625	–	// check for and ignore blank lines
626	–	if ( read_buffer != NULL )
627	–	tempZangs.push_back( atof(read_buffer) );
628	–	eof_test = fgets(read_buffer, sizeof(read_buffer), inAngFile);
629	–	}
630	–
631	–	// Check to see that the number of integrable objects in the
632	–	// intial configuration file is the same as derived from the
633	–	// meta-data file.
634	–	if( nTotObjs != tempZangs.size() ){
635	–	sprintf( painCave.errMsg,
636	–	"RestraintReader zAngle reading Error. %s nIntegrable, %d, "
637	–	"does not match the meta-data file's nIntegrable, %d.\n",
638	–	inAngFileName.c_str(), tempZangs.size(), nTotObjs);
639	–	haveError= 1;
640	–	simError();
641	–	}
642	–
643	–	// At this point, node 0 has a tempZangs vector completed, and
644	–	// everyone else has nada
645	–
646	–	for (i=0 ; i < info_->getNGlobalMolecules(); i++) {
647	–	// Get the Node number which has this atom
648	–	which_node = info_->getMolToProc(i);
649	–
650	–	if (which_node == masterNode) {
651	–	mol = info_->getMoleculeByGlobalIndex(i);
652	–
653	–	if(mol == NULL) {
654	–	strcpy(painCave.errMsg, "Molecule not found on node 0!");
655	–	haveError = 1;
656	–	simError();
657	–	}
658	–
659	–	for (integrableObject = mol->beginIntegrableObject(ii);
660	–	integrableObject != NULL;
661	–	integrableObject = mol->nextIntegrableObject(ii)){
662	–	intObjIndex = integrableObject->getGlobalIndex();
663	–	integrableObject->setZangle(tempZangs[intObjIndex]);
664	–	}
665	–
666	–	} else {
667	–	// I am MASTER OF THE UNIVERSE, but I don't own this molecule
668	–	// listen for the number of integrableObjects in the molecule
669	–	MPI_Recv(&nCurObj, 1, MPI_INT, which_node,
670	–	TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
671	–
672	–	for(j=0; j < nCurObj; j++){
673	–	// listen for which integrableObject we need to send the value for
674	–	MPI_Recv(&intObjIndexTransfer, 1, MPI_INT, which_node,
675	–	TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
676	–	angleTransfer = tempZangs[intObjIndexTransfer];
677	–	// send the value to the node so it can initialize the object
678	–	MPI_Send(&angleTransfer, 1, MPI_REALTYPE, which_node,
679	–	TAKE_THIS_TAG_DOUBLE, MPI_COMM_WORLD);
680	–	}
681	–	}
682	–	}
683	–	} else {
684	–	// I am SLAVE TO THE MASTER
685	–	for (i=0 ; i < info_->getNGlobalMolecules(); i++) {
686	–	int which_node = info_->getMolToProc(i);
687	–
688	–	if (which_node == worldRank) {
689	–
690	–	// BUT I OWN THIS MOLECULE!!!
691	–
692	–	mol = info_->getMoleculeByGlobalIndex(i);
693	–
694	–	if(mol == NULL) {
695	–	sprintf(painCave.errMsg,
696	–	"RestReader Error: molecule not found on node %d\n",
697	–	worldRank);
698	–	painCave.isFatal = 1;
699	–	simError();
700	–	}
701	–
702	–	nCurObj = mol->getNIntegrableObjects();
703	–	// send the number of integrableObjects in the molecule
704	–	MPI_Send(&nCurObj, 1, MPI_INT, 0,
705	–	TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
706	–
707	–	for (integrableObject = mol->beginIntegrableObject(ii);
708	–	integrableObject != NULL;
709	–	integrableObject = mol->nextIntegrableObject(ii)){
710	–	intObjIndexTransfer = integrableObject->getGlobalIndex();
711	–	// send the global index of the integrableObject
712	–	MPI_Send(&intObjIndexTransfer, 1, MPI_INT, 0,
713	–	TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
714	–	// listen for the value we want to set locally
715	–	MPI_Recv(&angleTransfer, 1, MPI_REALTYPE, 0,
716	–	TAKE_THIS_TAG_DOUBLE, MPI_COMM_WORLD, &istatus);
717	–
718	–	integrableObject->setZangle(angleTransfer);
719	–	}
720	–	}
721	–	}
722	–	}
723	–	#endif
440		}
725	–
726	–	void RestReader :: zeroZangle(){
727	–
728	–	int i;
729	–	unsigned int j;
730	–	int nTotObjs; // the number of atoms
731	–
732	–	Molecule* mol;
733	–	StuntDouble* integrableObject;
734	–	SimInfo::MoleculeIterator mi;
735	–	Molecule::IntegrableObjectIterator ii;
736	–
737	–	std::vector<StuntDouble*> vecParticles;
738	–
739	–	#ifndef IS_MPI
740	–	// set all zAngles to 0.0
741	–	for (mol = info_->beginMolecule(mi); mol != NULL;
742	–	mol = info_->nextMolecule(mi))
743	–
744	–	for (integrableObject = mol->beginIntegrableObject(ii);
745	–	integrableObject != NULL;
746	–	integrableObject = mol->nextIntegrableObject(ii))
747	–	integrableObject->setZangle( 0.0 );
748	–
749	–
750	–	// MPI Section of code..........
751	–	#else //IS_MPI
752	–
753	–	// first thing first, suspend fatalities.
754	–	painCave.isEventLoop = 1;
755	–
756	–	int masterNode = 0;
757	–	int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
758	–	int haveError;
759	–	int which_node;
760	–
761	–	MPI_Status istatus;
762	–
763	–	int nCurObj;
764	–	RealType angleTranfer;
765	–
766	–	nTotObjs = info_->getNGlobalIntegrableObjects();
767	–	haveError = 0;
768	–	if (worldRank == masterNode) {
441
442	<	for (i=0 ; i < info_->getNGlobalMolecules(); i++) {
443	<	// Get the Node number which has this atom
772	<	which_node = info_->getMolToProc(i);
773	<
774	<	// let's let node 0 pass out constant values to all the processors
775	<	if (worldRank == masterNode) {
776	<	mol = info_->getMoleculeByGlobalIndex(i);
777	<
778	<	if(mol == NULL) {
779	<	strcpy(painCave.errMsg, "Molecule not found on node 0!");
780	<	haveError = 1;
781	<	simError();
782	<	}
783	<
784	<	for (integrableObject = mol->beginIntegrableObject(ii);
785	<	integrableObject != NULL;
786	<	integrableObject = mol->nextIntegrableObject(ii)){
787	<
788	<	integrableObject->setZangle( 0.0 );
789	<
790	<	}
791	<
792	<	} else {
793	<	// I am MASTER OF THE UNIVERSE, but I don't own this molecule
794	<
795	<	MPI_Recv(&nCurObj, 1, MPI_INT, which_node,
796	<	TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
797	<
798	<	for(j=0; j < nCurObj; j++){
799	<	angleTransfer = 0.0;
800	<	MPI_Send(&angleTransfer, 1, MPI_REALTYPE, which_node,
801	<	TAKE_THIS_TAG_DOUBLE, MPI_COMM_WORLD);
802	<
803	<	}
804	<	}
805	<	}
806	<	} else {
807	<	// I am SLAVE TO THE MASTER
808	<	for (i=0 ; i < info_->getNGlobalMolecules(); i++) {
809	<	int which_node = info_->getMolToProc(i);
810	<
811	<	if (which_node == worldRank) {
812	<
813	<	// BUT I OWN THIS MOLECULE!!!
814	<	mol = info_->getMoleculeByGlobalIndex(i);
815	<
816	<	if(mol == NULL) {
817	<	sprintf(painCave.errMsg,
818	<	"RestReader Error: molecule not found on node %d\n",
819	<	worldRank);
820	<	painCave.isFatal = 1;
821	<	simError();
822	<	}
823	<
824	<	nCurObj = mol->getNIntegrableObjects();
825	<
826	<	MPI_Send(&nCurObj, 1, MPI_INT, 0,
827	<	TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
828	<
829	<	for (integrableObject = mol->beginIntegrableObject(ii);
830	<	integrableObject != NULL;
831	<	integrableObject = mol->nextIntegrableObject(ii)){
832	<
833	<	MPI_Recv(&angleTransfer, 1, MPI_REALTYPE, 0,
834	<	TAKE_THIS_TAG_DOUBLE, MPI_COMM_WORLD, &istatus);
835	<	vecParticles[j]->setZangle(angleTransfer);
836	<	}
837	<	}
838	<	}
839	<	}
840	<	#endif
841	<	}
842	<
843	<	} // end namespace oopse
442	>
443	>	}//end namespace OpenMD

Comparing:
trunk/src/io/RestReader.cpp (property svn:keywords), Revision 990 by chrisfen, Mon Jun 19 01:36:06 2006 UTC vs.
branches/development/src/io/RestReader.cpp (property svn:keywords), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

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